Sci & Educ (2011) 20:453471

DOI 10.1007/s11191-010-9267-6

Why Machine-Information Metaphors are Bad

for Science and Science Education

Massimo Pigliucci Maarten Boudry

Published online: 11 June 2010

 Springer Science+Business Media B.V. 2010

Abstract Genes are often described by biologists using metaphors derived from computa-
tional science: they are thought of as carriers of information, as being the equivalent of
blueprints for the construction of organisms. Likewise, cells are often characterized as
factories and organisms themselves become analogous to machines. Accordingly, when the
human genome project was initially announced, the promise was that we would soon know
how a human being is made, just as we know how to make airplanes and buildings. Impor-
tantly, modern proponents of Intelligent Design, the latest version of creationism, have
exploited biologists use of the language of information and blueprints to make their spurious
case, based on pseudoscientific concepts such as irreducible complexity and on flawed
analogies between living cells and mechanical factories. However, the living organ-
ism = machine analogy was criticized already by David Hume in his Dialogues Concerning
Natural Religion. In line with Humes criticism, over the past several years a more nuanced and
accurate understanding of what genes are and how they operate has emerged, ironically in part
from the work of computational scientists who take biology, and in particular developmental
biology, more seriously than some biologists seem to do. In this article we connect Humes
original criticism of the living organism = machine analogy with the modern ID movement,
and illustrate how the use of misleading and outdated metaphors in science can play into the
hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors
will improve both the science of biology and its understanding by the general public.

To the few this is as clear as daylight, and beautifully suggestive,

but to many it is evidently a stumbling-block.
(Alfred Russel Wallace to Charles Darwin, on the use of the metaphor of natural
selection)

M. Pigliucci (&)
Department of Philosophy, CUNY-Lehman College, Carman Hall 360, 250 Bedford Park Blvd West,
Bronx, NY 10468, USA
e-mail: massimo.pigliucci@lehman.cuny.edu
URL: www.platofootnote.org

M. Boudry
Department of Philosophy & Moral Sciences, Ghent University, Blandijnberg 2, 9000 Ghent, Belgium

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454 M. Pigliucci, M. Boudry

The price of metaphor is eternal vigilance.

(A. Rosenblueth and N. Wiener, cited in Robert Root-Bernsteins Metaphorical
Thinking, American Scientist Nov/Dec 2003)

1 Introduction: The Machine Metaphor in Biological Science and Education

Scientific thinking and education are rife with the use of metaphors. Well-known examples
include physics (heavy objects on a blanket as an image of spacetime curvature),
chemistry (atoms as miniature solar systems), ecology (the planet Earth as a homeostatic
organism), and many others (Condit et al. 2002; Brown 2003). In biology and biological
education in particular, metaphors are pervasive at almost every level of description and
explanation. Brown (2003, p. 159) has even argued that biology today reveals more
forcefully than any other area of science the essential role of metaphor in scientific rea-
soning and communication. Perhaps this pervasiveness of metaphors is an inevitable
result of the way human beings think (Lakoff and Johnson 1980; De Cruz and De Smedt
2010), but it has consequences for both science education and scientific research, and not
necessarily for the better. For instance, Fox Keller (1995) made that case concerning
information-type metaphors in the broad field of genetics (see also Nelkin 2001), while
Martin (1994) has done the same for the more specific area of immunology and HIV-AIDS
research.
The simple empirical observation that science talk depends heavily on analogical
thinking mandates that we examine the consequences of deploying certain metaphors on
how students and the public at large end up understanding science, and that we be attentive
to the way pseudoscientists often seize upon these metaphors to foster misunderstandings.
Specifically, if we want to keep Intelligent Design out of the classroom, not only do we
have to exclude the theory from the biology curriculum, but we also have to be weary of
using scientific metaphors that bolster design-like misconceptions about living systems.
We argue that the machine-information metaphor in biology not only misleads students
and the public at large, but cannot but direct even the thinking of the scientists involved,
and therefore the sort of questions they decide to pursue and how they approach them. For
instance, there undoubtedly were very good reasons to pursue the Human Genome Project
during the 1990s and the early part of the 21st century, but obtaining the blueprint for
how human beings are made (and therefore cure genetic-based diseases like cancer) was
certainly not one of those good reasons. Yet, it was the blueprint rhetoricbased on the
actual informatics-directed thinking of the scientists involvedthat helped sell the 4.2
billion effort (in 2009 dollars) to the American public,1 not to mention redirect the research
time and intellectual efforts of tens of thousands of scientists and graduate students the
world over.
Similarly, the never ending debate in science education between creationists and evo-
lutionary biologists hinges on the persistent (mis-)understanding of biological organisms as
machines, an understanding that is perpetuated by biologists themselves in textbooks
and lectures. The organism-as-machine metaphor goes much further back in time than the
decidedly modern genome-as-blueprint one, to Rene Descartes and other mechanistic
philosophers. Interestingly, as we shall see, attempts to point out its misleading effects are
also quite old, beginning with David Humes devastating critique of the idea of intelligent
design.

1
See http://www.genome.gov/11006943.

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Why Machine-Information Metaphors are Bad for Science 455

In this paper we discuss the effect of what we call the machine-information metaphor
(or family of metaphors, to be more precise) in the areas of science education and scientific
research. In the first case, we examine the debate about Intelligent Design and argue that
some defenders of evolution themselves (unwittingly) keep fueling the widespread mis-
understanding among the general public, because they accept the fundamental soundness
of their opponents characterization of organisms as machine-like. In the second case, we
argue that thinking of genomes as blueprints has not only led the general public astray but
may have also delayed the incorporation of developmental biology into evolutionary
theory, and is still delaying the expansion of the general concept of heritable information to
phenomena that rightly should fall within its purview, like epigenetic, behavioral, cultural
and even environmental transgenerational effects. We conclude with a brief look at a few
alternative metaphors and suggest that biological research and teaching could and should
actually be done without much use of metaphorical thinking, although the widespread
tendency to employ the latter may be used as a critical thinking tool in both general and
graduate level education to produce more science-savvy citizens and scientists.

2 Machine Metaphors, Intelligent Design and Science Education

When delving into unknown territory, scientists have often naturally relied on their
experiences in more familiar domains to make sense of what they encounter (De Cruz &
De Smedt 2010). In the early days of the scientific revolution, mechanical metaphors
proved to be a powerful instrument to get a grip on new discoveries about the living world
and the universe at large. According to Niall Shanks, we can trace back the emergence of
machine metaphors at least to the Middle Ages, when new achievements of technology had
a profound cultural influence and captured the collective imagination (Shanks 2004, pp.
257). Against this background of technological innovation, it is not surprising that the
pioneers of anatomy and physiology relied on the metaphor of the animal body as a
complicated piece of machinery to make sense of their discoveries. The mechanical lan-
guage provided a richness of meaning and allowed them to structure the new phenomena in
terms of familiar experiences (Lakoff and Johnson 1980). For example, the image of the
human heart as a pump with intricate mechanical components played an important role in
William Harveys discoveries about blood circulation.
In the course of the 17th century, a new philosophy of nature became prominent that
developed a conception of the universe in purely mechanical terms. According to this
mechanical philosophy, which was developed by thinkers like Rene Descartes, Pierre
Gassendi and Robert Boyle, the phenomena of nature can be understood purely in terms of
mechanical interactions of inert matter (Ashworth 2003). This mechanization of nature
proved an important driving force behind the Scientific Revolution, and at the end of the
17th century culminated in Newtons theory of motion. Newtons description of planetary
orbits following the fixed laws of gravity conveyed an image of a clockwork universe set in
motion by an intelligent First Cause. In fact, that was exactly how Newton conceived the
universe and its relation to the Creator. For Newton and many of his contemporaries, the
importance of the mechanical conception of nature was greater than the mere term
metaphor would suggest, as the development of mechanistic philosophy was itself largely
inspired by religious motivations (Ashworth 2003). As Shanks wrote in his account of the
history of the design argument, the very employment of machine metaphors invited
theological speculation (Shanks 2004, p. 32).

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In the second part of the 17th century, the mechanical pictures of living organisms and
of the cosmos at large converged into an intellectual tradition where theology and science
were intimately intertwined: natural theology. The most famous representative of this
tradition was William Paley, whose work Natural Theology, of Evidence of Existence and
Attributes of the Deity, Collected from the Appearances of Nature (1802) made a deep
impression on the young Charles Darwin. As the title of the book makes clear, Paley and
the natural theologians conceived of Nature as a complicated machinery of intricate wheels
within wheels, in which every organism has its proper place and is adapted to its envi-
ronment. According to Paley, the contrivance and usefulness of parts exhibited by living
organisms attests to the intelligence and providence of a benevolent Creator. This so-called
design argument already had a long intellectual pedigree, dating back to Plato, Cicero and
Thomas Aquinas, but its most famous formulation is found in the first chapter of Natural
Theology, in which Paley relies on the analogy between living organisms and a pocket
watch to support his design inference.2
In crossing a heath, suppose I pitched my foot against a stone, and were asked how
the stone came to be there: I might possibly answer, that for any thing I know to the
contrary, it had lain there for ever: nor would it perhaps be very easy to show the
absurdity of this answer. But suppose I had found a watch upon the ground, and it
should be inquired how the watch happened to be in that place; I should hardly think
of the answer which I had before given, that for any thing I knew, the watch might
have always been there. Yet why should not this answer serve for the watch, as well
as for the stone? Why is it not as admissible in the second case as in the first? For this
reason, and for no other, viz., that when we come to inspect the watch, we perceive
(what we could not discover in the stone) that its several parts are framed and put
together for a purpose This mechanism being observed the inference, we think,
is inevitable, that the watch must have had a maker; that there must have existed, at
some time, and at some place of other, an artificer or artificers, who formed it for the
purpose which we find it actually to answer; who comprehended its construction, and
designed its use. (Paley 1802, p. 5)
The idea is that without having witnessed the creation of the watch, without even
knowing anything about the identity of the designer, the purposeful arrangement of parts
forces the conclusion of intelligent design on the observer. Of course, there is at least one
fundamental dissimilarity: human artefacts do not propagate, whereas living organisms do.
However, Paley did not think this significantly endangers the analogy. Instead, he argued
that it actually strengthens the design inference for the case of living organisms. After all,
continues Paley, suppose that the watch we found in the heath did not only indicate the
time, but was also capable of producing another watch with the same features. Would not
this even more increase [our] admiration of contrivance? (Paley 1802, p. 9) Living
organisms, according to Paley, surpass the ingenuity and complexity of human artefacts
in a degree which exceeds all computation (Paley 1802, p. 13), and are worthy of a
divine Creator alone. Even Kant, in his Critique of Judgment, clearly struggled with the
apparently purposeful design of living organisms. Although he was wary of teleological
accounts, always preferring efficient mechanical causes for explaining the world, he

2
Paley was not the first to pursue the analogy with a pocket watch. In fact, Paley borrowed the famous
paragraph in the first chapter of his work from the book Regt gebruik der werelt beschouwingen (1715) by
the Dutch physician Bernard Nieuwentijt, who was himself probably influenced by thinkers like William
Derham, John Ray and Robert Boyle.

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Why Machine-Information Metaphors are Bad for Science 457

acknowledged that living systems necessarily had to be explained as if they were

teleological in nature. Thus, he maintained that it is absurd to hope that another Newton
will arise in the future who shall make comprehensible by us the production of a blade of
grass according to natural laws which no design has ordered (Kant 2007, 185). It seems
that for beings such as ourselves, used to associate complexity with intelligence, it is very
difficult to escape the impression of design in nature, and the adaptive complexity of living
organisms certainly demands a special explanation. Darwins theory of evolution by nat-
ural selection eventually provided such explanations, fatally undermining Paleys argu-
ment, and flagrantly contradicting Kants pessimism on the matter.
While Darwin was the one who gave the most decisive blow to the design argument by
suggesting a natural explanation for adaptive complexity in the living world, many phi-
losophers would agree that David Hume foreshadowed its demise, by exposing several
problems with the central analogy. In his work Dialogues Concerning Natural Religion
(Hume 1779), which actually predates Paleys magnum opus by more than 50 years, we
find a discussion of the design argument among Philo, the skeptical character that voices
Humes ideas, Demea, the orthodox religious believer, and Cleanthes, the advocate of
natural theology.
After Cleanthes has set out the design argument in terms foreshadowing Paleys analogy
of the watch, Philo objects that it is dangerous to derive conclusions about the whole of the
universe on the basis of a spurious analogy with one of its parts. Given that our experience
with design is limited to human artifacts only, we have to proceed with great caution, and it
would be presumptuous to take so minute and select a principle as the human mind as the
model for the origin of the whole universe.3 Hume realized that, at least in some cases,
appearances of intelligent design can be deceptive. In the words of Philo:
If we survey a ship, what an exalted idea must we form of the ingenuity of the
carpenter who framed so complicated, useful, and beautiful a machine? And what
surprise must we feel, when we find him a stupid mechanic, who imitated others, and
copied an art, which, through a long succession of ages, after multiplied trials,
mistakes, corrections, deliberations, and controversies, had been gradually improv-
ing? (Hume 1998 [1779], p. 36)
In contemplating that [m]any worlds might have been botched and bungled,
throughout an eternity, ere this system was struck out, Hume even comes close to Dar-
wins crucial insight about the power of natural selection. (Ibid, p. 36)
Although Hume does not deny that we can discern similarities between nature and
human artifacts, he warns us that the analogy is also defective in several respects. And if
the effects are not sufficiently similar, conclusions about similar causes are premature. To
illustrate this, Philo proposes another possible cosmogony on the basis of the analogy
between the world and an animal:
A continual circulation of matter in [the universe] produces no disorder; a continual
waste in every part is incessantly repaired: The closest sympathy is perceived
throughout the entire system: And each part or member, in performing its proper
offices, operates both to its own preservation and to that of the whole. The world,
therefore, I infer, is an animal. (Hume 1998 [1779], p. 39)

3
Philo says that it is a palpable and egregious partiality to confine our view entirely to that principle by
which our own minds operate (Hume 1998 [1779], p. 46).

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Philo further speculates that the world even more resembles a plant, and that it could
have come into existence by a process analogous to reproduction or vegetation. While the
others protest at his arbitrary speculations, Philo maintains that his analogies, though
certainly defective in some respects, are no more so than the machine analogy. [I]n such
questions as the present, a hundred contradictory views may preserve a kind of imperfect
analogy, and invention has here the full scope to exert itself (Hume 1998 [1779], p. 49).
Aware of the fallibility and imperfections of human reasoning, Hume remains highly
skeptical about the design inference and the machine analogy, even though he was not able
to provide a satisfactory explanation for the appearance of design in nature.
In The Origin of Species, Charles Darwin (1859) finally proposed a natural explanation
for the phenomenon that inspired Paley but failed to convince Hume. Although the design
argument is still of interest to philosophers and historians of science, it has been widely
discarded in the scientific community. However, the analogy on which Paley based his
inference seems to be alive and well, not only in the minds of creationists and ID pro-
ponents, but also in the writings of science popularizers and educators (and even in actual
scientific work, as we will see in the next section). Many scientists have actually argued
that Paley at least offered an incisive formulation of the problem as there is indeed a hard-
to-shake intuition of contrivance and intelligent design in nature. As one of the most ardent
defenders and popularizers of evolutionary theory put it, Biology is the study of com-
plicated things that give the appearance of having been designed for a purpose (Dawkins
1991, p. 1). Adaptive complexity, then, is still regarded as something that requires a special
explanation.
In textbooks, science educators have presented the comparison of living organisms and
man-made machines not just as a superficial analogy, but carrying it out to a considerable
level of detail. For example, the cell has been described as a miniature factory, complete
with assembly lines, messengers, transport vehicles, etc. Consider the following quote from
Bruce Alberts, former president of the National Academy of Sciences:
The entire cell can be viewed as a factory that contains an elaborate network of
interlocking assembly lines, each of which is composed of a set of large protein
machines. Why do we call the large protein assemblies that underlie cell function
protein machines? Precisely because, like machines invented by humans to deal
efficiently with the macroscopic world, these protein assemblies contain highly
coordinated moving parts. Given the ubiquity of protein machines in biology, we
should be seriously attempting a comparative analysis of all of the known machines,
with the aim of classifying them into types and deriving some general principles for
future analyses. Some of the methodologies that have been derived by the engineers
who analyze the machines of our common experience are likely to be relevant.
(Alberts 1998, p. 291)
Similarly, in their popular high school textbook Biology, Kenneth Miller and Joe Levine
develop an extensive analogy between the living cell and a manufacturing plant (Levine
and Miller 1994). In Millers own words:
The nucleus is the factorys main office, the mitochondria its power plants, the
ribosomes its manufacturing equipment, and the Golgi apparatus its shipping and
receiving department. (Miller 2008, p. 27)
In line with the machine metaphor, scientists have also conceived of the genome as a
blueprint for the organism, written in a four-letter alphabet and in a language that sci-
entists have deciphered. In the wake of the Humane Genome Project, many scientists have

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Why Machine-Information Metaphors are Bad for Science 459

enthusiastically described the human DNA sequence as the book of life or the blueprint
for a human being (for an overview, see Nelkin 2001). In an interview for Time about the
Human Genome Project, biochemist Robert Sinsheimer has described the genome as the
complete set of instructions for making a human being [] written in the language of
deoxyribonucleic acid, the fabled DNA molecule (Jaroff 1989). According to Miller,
machine metaphors are useful because they allow teachers to get across complicated
material, since they are easy to remember and make scientific sense (Miller 2008, p. 27).
However, we will see that analogies between living organisms and machines or programs
(what we call machine-information metaphors) are in fact highly misleading in several
respects. Bearing in mind that metaphors are powerful persuasive tools that can deeply
affect the way we look at the world, we think the pervasiveness of extensive machine
analogies in science education is in fact unfortunate.
Creationists and their modern heirs of the Intelligent Design movement have been eager
to exploit mechanical metaphors for their own purposes (Perakh 2008). For example, Bruce
Alberts description of the living cell as a factory has been approvingly quoted by both
Michael Behe and William Dembski, two leading figures in the ID movement. For ID
proponents, of course, these are not metaphors at all, but literal descriptions of the living
world, arching back to Newtons conception of the Universe as a clock-like device made
by the Creator. The very fact that scientists rely on mechanical analogies to make sense of
living systems, while disclaiming any literal interpretation, strengthens creationists in their
misconception that scientists are blinded by a naturalistic prejudice. And of course, the
idea of a genomic blueprint is highly congenial to the theistic worldview4 of ID pro-
ponents. In the creationist textbook Of Pandas and People, which has been proposed by ID
advocates as an alternative to standard biology textbooks in high school, we read that
Intelligent design [] locates the origin of new organisms in an immaterial cause: in a
blueprint, a plan, a pattern, devised by an intelligent agent (Davis et al. 1993, p. 14).5
The analogy between living organisms and man-made machines has proven a persua-
sive rhetorical tool of the ID movement (for a thorough examination of ID theory, see
Pennock 1999; Pigliucci 2002; Shanks 2004). In fact, for all the technical lingo and
mathematical demonstrations, in much of their public presentations it is clear that ID
theorists actually expect the analogies to do the argumentative work for them (Young
2004). In Darwins Black Box, Behe takes Alberts machine analogy to its extreme,
describing the living cell as a complicated factory containing cargo-delivery systems,
scanner machines, transportation systems and a library full of blueprints. Here is a typical
instance of Behes reasoning:
In the main area [cytoplasm] are many machines and machine parts; nuts, bolts, and
wires float freely about. In this section reside many copies of what are called master
machines [ribosomes], whose job it is to make other machines. They do this by
reading the punch holes in a blueprint [DNA], grabbing nuts, bolts, and other parts
that are floating by, and mechanically assembling the machine piece by piece. (Behe
2006, pp. 1045)
Behes favorite model of biochemical systems is a mechanical mousetrap, the familiar
variant consisting of a wooden platform, a metal hammer, a spring etc. According to Behe,

4
A survey by Condit et al. about the perception of the blueprint and recipe metaphor suggests that deeply
religious people prefer the blueprint metaphor precisely because of its theistic connotations (Condit et al.
2002, p. 312).
5
Thanks to Stefaan Blancke for this suggestion.

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460 M. Pigliucci, M. Boudry

if any one of these components is missing, the mousetrap is no longer able to catch mice.
He has termed this interlocking of parts irreducible complexity and thinks it charac-
terizes typical biochemical systems. As Shanks wrote: [t]he mousetrap is to Behe what
the well-designed pocket watch was for Paley (Shanks 2004, p. 165). But whereas Paley
can be excused on the grounds of the state of scientific knowledge in the 18th century, for
Behe the situation is a little different. Modern biochemistry, nota bene Behes own dis-
cipline, has revealed that biochemical systems are not like mechanical artifacts at all (see
our discussion of brittleness below; also Shanks and Joplin 1999). Moreover, even
biological systems that are irreducibly complex under Behes definition pose no problem
for evolution by natural selection, see for example Miller (2000).
ID proponents have buttressed their analogies between living systems and mechanical
contraptions with a lot of visual rhetoric as well. The flagellum of the bacterium E. coli, the
hallmark of the ID movement, has been represented as a full-fledged outboard rotary
motor, with a stator, drive shaft, fuel supply etc. It features on the cover of Dembskis book
No Free Lunch and has been used numerous times in presentations and online articles. The
idea seems to be that if it looks designed, it has to be designed. But as Mark Perakh has
documented, ID supporters invariably use idealized and heavily stylized representations of
the flagellum, in order to make it more resemble a man-made contraption (Perakh 2008).
Another striking example of this visual rhetoric is a new video by Discovery Institute
president Stephen C. Meyer,6 which presents a computer-simulatedand again heavily
stylizedjourney inside the cell, and describes the biochemical processes in terms of
digital characters in a machine code, information-recognition devices and
mechanical assembly lines. Meyer commented that evolutionists will have a hard time
now dissuading the public from the fact that the evidence for design literally unfolds
before them.
Of course, the mere observation that creationists have seized on machine metaphors in
biology does not suffice to demonstrate that these metaphors do not make scientific sense.
However, the fact that they tend to do so systematically, using full-length quotes from
respectable scientists, should make us weary of the possible dangers of misleading met-
aphors. If the rhetoric of the ID movement is demonstrably based on these mechanical
analogies, it can be instructive to reexamine their scientific merits. In the next section, we
argue that the machine-information analogy has indeed influenced the way scientists
themselves think about biological structure, function, and evolution. By analyzing the
consequences of and reactions to this analogy in actual biological research, we show that
its scientific merits are very week indeed, and that its place in modern biology has become
questionable.

3 Machine Metaphors and the Practice of Biological Research

The idea of organism as a machine, a device that stores and acts on information, has
permeated not just education about biological science, but the practice of that science
itself. Descartes (1648) in LHomme developed the fundamental idea that living organ-
isms, including human beings (but in the latter only as far as the vegetative aspects of
the body are concerned) are machines, whose function can be understood in terms of
simple mechanical forces and interactions. This was part of Descartes overall program of
countering Aristotelian science and developing a new physics based on the mechanical

6
See http://www.journeyinsidethecell.com/.

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Why Machine-Information Metaphors are Bad for Science 461

philosophy that was inspiring Galilei and later found full fruition in Newton, giving birth
to what we recognize as modern science. Biology, however, has always also been char-
acterized by the presence of an anti-reductionist, vitalistic streak, which ironically peri-
odically arches back to Aristotle (350BE/1991) and his conception of vegetable and animal
souls as presented in his De Anima.
This back and forth between mechanistic and vitalistic conceptions of living organisms
characterized debates among biologists during the 19th century, when Darwins ideas can
be seen as certainly more mechanistic in nature than, say, those of Lamarck. The vitalistic
position gained new prominence again at the beginning of the 20th century, largely through
the efforts of Henri-Louis Bergson, but evolutionary biology kept moving steadily in a
mechanistic direction throughout the Modern Synthesis of the 19301940s (Mayr and
Provine 1998). The coup de grace was then given to vitalism by the onset of the molecular
revolution, first anticipated in Schrodingers What is Life? (1944) and then definitely
playing a determinant role in late 20th century biology after the discovery of the structure
of DNA (Watson and Crick 1953).
Ever since the 1950s what we might more properly call the machine-information
metaphor has been prevalent in molecular biology, largely because of the tremendous
success of the molecular revolution, throughout the biological sciences (despite continued
pockets of resistance within the more organismally oriented disciplines of biology, chiefly
ecology and evolutionary biology). It is sometimes argued by biologists that the use of
machine-information metaphors is limited to popular writings of the type discussed in the
previous section, and that they do not inform actual research papers. But this is quickly
dispelled by an even cursory examination of databases such as Web of Science or PubMed.
Let us take, for instance, the idea that genes are blueprints, i.e., that they contain the
information to build proteins or more broadly any aspect of the phenotype. Hassoun et al.
(2009) talk about differentiation of the principal body axes in the early vertebrate embryo
[being] based on a specific blueprint of gene expression and say that the mouse and
rabbit show distinct structural differences in APD [anterior pregastrulation differentiation]
and the[ir] molecular blueprint. Iimura et al. (2009) refer to the colinear disposition of
Hox genes expression domains [which] provides a blueprint for the regionalization of the
future vertebral territories of the spine in vertebrates. Uttamchandani et al. (2009) are
confident that the sequencing of the human genomes provided a wealth of information
about the genomic blueprint of a cell (though they do acknowledge that this does not
provide the entire story of life and living processes). Rutka et al. (2009) affirm that the
human genome project has been completed providing a blueprint for the human species.
Saminathan et al. (2009) maintain that their neuronal transcripts were further analyzed to
provide a genetic blueprint that can be used by neurobiologists to unravel the complex
cellular and molecular mechanisms underlying biological functions. And the list could
easily be extended to encyclopedic proportions.
One of the obvious patterns emerging from any such search of the recent literature is
that words like blueprint are rarely if ever used within the context of organismal (as
opposed to molecular) biological research, and indeed there is a sustained effort on the part
of (some) ecologists and evolutionary biologists to counter what they see as the hyper-
reductionist approach brought about by the molecular revolution. This is particularly
evident when we focus on ongoing discussions on the scope and results of evo-devo
(evolution of development), the relatively new field that is supposed precisely to bridge the
gap between organismal and molecular biology, all the while finally bringing develop-
mental biology into the broad fold of the standard theory of evolution known as the

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Modern Synthesis (e.g., Minelli and Fusco 2005; Love 2006; Hendrikse et al. 2007; Muller
2007; Pigliucci 2009). This resistance against the machine-information metaphor, how-
ever, cannot and should not be read as a resurgence of vitalism, as no evo-devo author has
moved in that direction. Rather, it is the result of a genuine tension between the undeniable
successes of the molecular-reductionist approach on the one hand, and the limits that such
approach seems to reach when it tackles issues pertinent to the structure and evolution of
complex phenotypes.
We argue that part of this tension is in fact the result of, or is at least fostered by, the
deployment of the machine-information metaphor as a guiding idea of the molecular
biological research program (see the sample of recent references provided above), and that
new ways of thinking about development and evolution are building a conceptual
vocabulary that increasingly distances itself from the machine-information metaphor. Let
us consider two broad categories of examples, what we will be referring to as the problem
of development and the problem of environment.
The problem of development has arguably been present in one form or another
throughout the history of biology, and in modern shape constitutes the central aim of the
research program in evo-devo. If living organisms are sufficiently analogous to pro-
grammable machines, then the problem of development largely reduces to identifying
which pieces of the program (i.e., genes) control which parts of the hardware to be
assembled (the organism itself). That this is a line of inquiry actually pursued by biologists
over the past few decadesand not just a matter of idle talkis evident from the
bewildering literature on genes for a particular phenotype, even though the very notion
of a gene being for a phenotype is in fact justified only in very restricted cases (Kaplan
and Pigliucci 2001). While it can certainly be argued that the approach has been successful,
in reality that success is largely limited to one of two areas: the identification of few
complex phenotypic traits that do show a relatively simple mapping between genotype
and phenotype (e.g., eye color in vertebrates, see Sturm and Larsson 2009), or the cata-
loguing of large numbers of genes affecting a given phenotype (often, in the case of
humans, a disease-related one), where however each genetic element statistically accounts
for a minute fraction of the variation in the phenotype, and often only in a particular subset
of populations within a given species (Tian et al. 2008; Wu and Zhao 2009).
Recent advancements in theoretical biology and computational science may help us to
articulate the fundamental reasons why the problem of development cannot be solved by
more and better Genotype ) Phenotype mapping. Ciliberti et al. (2007) have pointed out
that direct encoding systems, such as human-designed software, suffer from brittle-
ness, that is they break down if one or a few components stop working, as a result of the
direct mapping of instructions to outcomes. If we think of living organisms as based on
genetic encoding systemslike blueprintswe should also expect brittleness at the phe-
notypic level which, despite the claims of creationists and ID supporters that we have
encountered above, is simply not observed. On the contrary, biological developmental
systems tend to be very robust to both internal (i.e., genetic) and external (i.e., environ-
mental) perturbations. In other words, pace Behe and other ID advocates, removing one
component in a complex biochemical pathway typically does not cause the system to
effectively cease functioning (Behe 2006, p. 39). Indeed, the fact that biological
organisms cannot possibly develop through a type of direct encoding of information is
demonstrated by calculations showing that the gap between direct genetic information
(about 30,000 protein-coding genes in the human genome) and the information required to
specify the spatial position and type of each cell in the body is of several orders of
magnitude (Stanley 2007). Where does the difference come from?

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Why Machine-Information Metaphors are Bad for Science 463

An answer that is being explored successfully is the idea that the information that makes
development possible is localized and sensitive (as well as reactive) to the conditions of the
immediate surroundings. In other words, there is no blueprint for the organism, but rather
each cell deploys genetic (Johannes et al. 2008) information and adjusts its status to signals
coming from the surrounding cellular environment, as well as from the environment
external to the organism itself. The way this works, then, is through two phases: in the
signaling phase information is deployed locally, within a given circuit (in computational
science models) or cell (in biological systems). The second phase is that of the expression
of a particular functional status, which depends on the input received so far by each circuit
or cell. In computational science, interestingly enough, this approach is known as
developmental encoding or artificial development and is in fact inspired by a more
realistic view of what sort of systems living organisms actually are (Hartmann et al. 2007).
One of the most interesting outcomes of shifting our thinking from direct/genetic
encoding to indirect/developmental encoding of information is that we then have an
immediate link between developmental biology and evolution: not only is research on
localized encoding showing it to be a better model for understanding development, but it
turns out that artificial systems based on developmental encoding are much more efficient
at searching for more robust solutions to whatever problem is posed to them, i.e., they
evolve faster than genetic encoding systems and produce phenotypes that are fault-toler-
antto use software engineering terminologybecause they are not brittle (Hartmann
et al. 2007): giving up talk of blueprints and computer programs immediately purchases an
understanding of why living organisms are not, in fact, irreducibly complex.
Developmental encoding has yet another advantage over genetic encoding, which is
proving interesting to software engineers while simultaneously shedding light on the way
living organisms develop: in the case of direct/genetic encoding, the length of the program
grows proportionally to the complexity of the phenotype, which quickly makes the system
unwieldy and again slows down its evolution. By comparison, indirect/developmental
encoding means that a relatively small number of instructions can produce a variety of
phenotypes, depending on the interactions among parts of the system and among these and
the external environment. Complex phenotypes, then, can be evolved without the necessity
to also evolve proportionally large genetic systems (Roggen et al. 2007). Looking at
evolution through these lenses may also provide us with insights into one of the funda-
mental questions in biology: why did development evolved in the first place? As it turns
out, when the phenotypes are simple, genetic and developmental encoding are roughly
equally efficient at evolving new solutions, because the genetic system is not too com-
plicated. It is only when more complex phenotypes are favored that the advantage of
indirect encoding becomes apparent (Roggen et al. 2007): perhaps this is why compara-
tively simpler life forms like bacteria do not need developmental encoding and better
approximate the simple Genotype ) Phenotype mapping assumed by the blueprint met-
aphor. But when evolution began to favorfor whatever reasonmore complex, multi-
cellular life forms, a new way of encoding information also evolved.
While much of the preceding discussion was framed in terms of the problem of
development, the second issue, which we referred to above as the problem of envi-
ronment is actually conceptually analogous and can be thought of in a similar fashion.
Biologists have known since immediately after the beginning of genetics, in 1900, that the
same genotype often develops different phenotypes in different environments. This is
difficult to make sense of if one thinks of genomes as a simple blueprint-like reservoir of
information. Accordingly, this phenomenonknown as phenotypic plasticity (Pigliucci

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2001)has remained largely in the background of biological research for most of the 20th
century.
During the last couple of decades, however, studies of phenotypic plasticity have taken
center stage in evolutionary biology, ecology, and even molecular biology, because of the
realization of the near-universality of the phenomenon. As usual, the initial approach to the
study of the genetic basis of plasticity was guided by the blueprint metaphor, with
researchers attempting to identify and map genes for plastic responses of a variety of
phenotypes to a variety of environmental conditions. It quickly became clear, however,
that plasticity is a complex developmental phenomenon, which requires a more nuanced
approach and is no different, in principle, from the study of any other complex outcome of
development. Indeed, if standard development can be thought of as the response of indi-
rect/developmental encoding to the internal environment surrounding each cell, then
plasticity can be seen as the similar response of indirect/developmental encoding to signals
originating in the environment external to the organism (Jablonka 2007).
If the problem of environment is conceptually analogous to the problem of develop-
ment, and both require a more sophisticated view of how organisms deploy genetic
information, then we begin to see the possibility that the notion of genetic information
itself is not quite so straightforward, and certainly is not one that fits comfortably with
ideas like blueprints and machines. Accordingly, biologists and philosophers of science
who have questioned the absolute centrality of genes inherent in the blueprint metaphor
have proposed new ideas that represent some of the current frontiers of theoretical evo-
lutionary biology. Let us briefly examine four of these, within the context of a broadened
perspective of inheritance and evolution that is facilitated by moving away from blueprint-
like thinking.
Mary Jane West-Eberhard (2003) has proposed that under certain circumstances genes
may not be the initiators of evolutionary change, as the standard version of evolutionary
theory maintains, but rather followers. The standard model assumes that new heritable
variation appears in a population of organisms because of either mutation or recombina-
tion, i.e., through genetic changes. This variation, if it has phenotypic outcomes that affect
fitness, is then selected for or against by natural selection, and populations evolve. But
according to the genes as followers model, sometime it is the external environment that
changes first, catalyzing the appearance of a number of new phenotypes through already
existing phenotypic plasticity. Should any of these phenotypes be adaptive, natural
selection would then favor the appearance of any new combination of genes that happen to
stabilize the plastic response. The crucial point is that under these circumstances (heritable)
plasticity allows the population to survive in a novel environment without any genetic
change. While in the long term evolution would still be a matter of gene-environment
interactions mediated by natural selection (because genes would eventually mold and fine-
tune the newly adaptive plastic response), at least some of the times the process would get
started by an environment-induced developmental change, not by a genetic one.
Eva Jablonka and Marion Lamb (2005) have gone in some sense a step further and
attempted to formalize a broader view of evolutionary change, which depends on the
existence of not one but four mechanisms of inheritance: first, the standard genetic system;
second, a panoply of epigenetic heritable effects, based on recently or newly discovered
phenomena, such as differential methylation of genes, alterations of chromatin structure,
so-called interference RNAs,7 and changes in conformation of proteins (e.g., prions), to

7
Methylation is a simple form of chemical alteration of DNA that affects gene expression; chromatin
structure refers to alteration in the spatial distribution of the DNA-proteins ensemble that makes up

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Why Machine-Information Metaphors are Bad for Science 465

mention a few; third, behavioral inheritance, mediated through the ability of some animal
species to mimic each others behavior without having it to be inscribed in their genes;
and fourth cultural inheritance, which is limited to humans and perhaps a few other species
of primates, but which has had an obviously disproportionate effect on the recent history of
our planet. Of course, it will be some time before theoretical population and quantitative
genetics will be able to get a handle on the cumulative and interactive effects of the non-
standard systems of inheritance, although work in that direction has already started
(Johannes et al. 2008; Slatkin 2009).
A third unorthodox idea about inheritance has been developed by some evolutionary
ecologists, and goes under the name of niche construction (Donohue et al. 2005; Laland
and Sterelny 2006). The basic concept is that organisms do not experience their envi-
ronment passively, but rather actively build their own niche at each generation. The
textbook example of this is beavers building dams, which not only represent artificial
environments for the beavers, but also affect the living of several other species in the local
community. A crucial point about niche construction is that it is made possible by the fact
that environmental materials and information are inherited along with the genes from
one generation of beavers to the next. Without this heritable set of background condi-
tions, the beaver genome simply could not enact the species-specific behavior of dam-
building.
Finally, some philosophers of science have taken all of the above to suggest that we
need to radically re-conceptualize the way we think of inheritance systems altogether.
They articulated what is known as Developmental Systems Theory (Oyama et al. 2003),
according to which genetic, epigenetic, behavioral, cultural and even environmental
information is inherited in parallel and intricately interconnected fashion, creating
cycles of causality which include the standard genetic mechanisms as just one of many
necessary (and none individually sufficient) causes.
The preceding discussion, we argue, shows that the limitations intrinsic in metaphors
such as genes as blueprints and the like are not just deleterious for science education
which would be bad enough. They actually misdirect or partially derail thinking about
what sort of research programs biologists ought to carry out and how. While there is no
question that the molecular revolution has been a central and positive development in
biology, and indeed in science in general, throughout the second part of the 20th century, it
is also becoming increasingly clear that the ultra-reductionist approach inspired and fueled
by machine-information metaphors is running out of steam and needs to be replaced with
more sophisticated and realistic thinking (a kind of reasonable, or non-greedy reduction-
ism, so to speak). Is it then time to retire metaphors like blueprints and machines, and to
seek an alternative way to conceptualize biological organisms, or would it perhaps be
better to abandon the use of metaphors in this field altogether?

4 The Search for New Metaphors

In their classic work on metaphors, Lakoff and Johnson argue that the basic function of
metaphorical concepts is to structure a new kind of experience in terms of a more familiar
and delineated experience (Lakoff and Johnson 1980). In science as well as in everyday

Footnote 7 continued
chromosomes; interference RNAs (iRNAs) are small molecules of ribonucleic acid that also affect gene
expression.

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466 M. Pigliucci, M. Boudry

language, metaphors highlight particular aspects of whatever it is we are trying to grasp,

but they will inevitably distort others. For example, the image of the tree of life, with new
species branching off as budding twigs and extinct species as dead branches, is an
instructive approximation of the relations of evolutionary descent. However, it can also
foster misconceptions about progress in evolution, or lead to a simplistic conception of
speciation events, or to a downplay of horizontal gene transfer and reticulate (i.e., by inter-
species hybridization) speciation events. To give one more example, in physical chemistry
the model of the atom as a miniature solar system, with electrons orbiting the nucleus as
planets, though still having wide public appeal, is fundamentally inaccurate.
Of course, no metaphor will do its job perfectly, but it is crucial to realize, as Lakoff and
Johnson (1980) have shown, that the widespread deployment of a particular metaphor can
have a feedback effect on the way we perceive things, not just how we present them to
others. In the examples discussed in this paper, the lure of machine-information metaphors
in the history of biology has invited scientists to think of genomes as blueprints for
organisms, written in the four-letter alphabet of DNA and readable in a manner analogous
to a computer code. But as we have argued, the machine-information conception of living
systems has led both the public and the scientific community astray.
In response to this problem, some scientists and science educators have proposed
several alternative and improved metaphors to characterize the relationship between
genotype and phenotype. Biologist Patrick Bateson, for instance, was probably the first to
compare the DNA sequence of living organisms with a recipe for a cake (Dawkins and
Wong 2005, p. 414). The idea of a genetic recipe has several advantages over the blueprint
metaphor, the most important being that it takes into account pleiotropy (one gene
affecting more than one trait) and epistasis (genegene interactions), and that it is more
sensitive to what we termed the problem of environment and the problem of development
in the previous section. As a consequence, the simple picture of a one-to-one (or close to)
correspondence between particular genes and phenotypic traits is abandoned, which
becomes clear when one considers that there is no way to locate particular ingredients in
individual crumbs of a cake (Dawkins 1991, pp. 2956). Accordingly, there is no possi-
bility of reverse-engineering the end product to the set of procedures (the recipe) that
made the final product possible. This has important consequences not just for science
education, but for research agendas, as the idea of reverse engineering is commonly
invoked everywhere from genomic studies to the understanding of the brain (though in the
latter case in a different sense from the one used in molecular biology: Pinker 1997).
Of course, if carried too far, the recipe metaphor can in turn be quite misleading. To get
the desired result, a cook has to lump together different ingredients in the correct pro-
portions, and follow a set of instructions for handling the dough and preparing the oven.
But as we saw, developmental encoding is an enormously more complex and very different
sort of procedure, which is also highly dependent on epigenetic factors and unpredictable
vagaries of the external environment. The expression of specific genes in the course of
development resembles nothing like the way a cook handles the ingredients of a recipe.
Living organisms are also highly differentiated in a number of functional parts or com-
ponents (cell types, tissues, etc.), in contrast with the homogenous cake that comes out of
the oven. Moreover, the genome is not written in anything like a language, as in the case
of a recipe, and it certainly does not contain a description of the desired end product in any
meaningful sense of the word description.
Condit et al. have discussed the recipe metaphor as an alternative to talk of blue-
prints, pointing out that it was adopted with surprising swiftness by science popu-
larizers and the media in the 1990s (Condit et al. 2002, p. 303). However, they also

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Why Machine-Information Metaphors are Bad for Science 467

remark that, as a new master metaphor to capture the relationship between genotype
and phenotype, the image of a recipe for a cake has little to recommend either. For
example, evoking recipes can invite people to think of the genome as a step-by-step
manual that describes how to make a human, in that sense falling into the same trap
as the idea of a blueprint.
That being said, if contrasted with the blueprint metaphor, the recipe metaphor conveys
the point about lack of one-to-one correspondence between genes and phenotypes very
well, and hence it highlights an important fact about development and the Geno-
type ) Phenotype map. If the recipe metaphor is used within this restricted context, for
example in explicit contrast with the characteristics of a blueprint, it is immediately clear
what are the salient points of connection with living systems, and people are less likely to
be misled by stretching the metaphor beyond usefulness. If the recipe metaphor is pre-
sented as an alternative to the blueprint, however, it is bound to mislead people no less than
its rival.
The same point applies to other interesting metaphors that have been proposed in this
context, for example Lewis Wolperts comparison of early embryonic development with
the Japanese art of origami (Wolpert and Skinner 1993; Dawkins and Wong 2005). The
analogy highlights the circuitous step-by-step development of the early embryo,8 but of
course in a piece of origami art the structure is imposed top-down from an intelligent agent,
whereas the functional differentiation in the embryo is regulated bottom-up by a complex
interaction between genes and environment. Moreover, origami simply fold to yield the
final product, which in a very real sense is already there from the beginning. This is
definitely not the way embryos develop, with their ability to respond to local and external
environmental fluctuations.
The general problem that we have been discussing seems to us to be not just that one
kind of metaphor or another is woefully inadequate to conceptualize biological organ-
isms and their evolution. It is that it simply does not seem to be possible to come up
with a metaphor that is cogent and appropriate beyond a very limited conceptual space.
Although some of the alternatives are more accurate than the blueprint metaphor (in
some respects), we certainly have not found one that we would recommend as a
replacement. Should we therefore try to avoid the use of metaphors in biological
teaching and research altogether? Or do we simply expect too much from metaphors in
science and education.

5 Conclusion: Metaphors as Teaching Moments in Scientific Research and Education

Analogical and metaphorical thinking is widespread among human beings, although of

course different cultures and historical moments inspire people to use different metaphors.
After all, a metaphor is an attempt to make sense of novel concepts by pairing them with
known ideas to increase our overall understanding. Metaphorical thinking is therefore part
of our language, and language is inextricably connected to our thinking, but to put it as
Wittgenstein did: It is, in most cases, impossible to show an exact point where an analogy
starts to mislead us (Wittgenstein 1972, p. 28). Yet a great part of doing philosophy
consists precisely in clarifying our language in an attempt to advance our thinking. To
quote Wittgenstein (1951, 109) again: Philosophy is a battle against the bewitchment of

8
See also the online video demonstration of origami embryology by Kathryn Tosney and Diana Darnell:
http://www.origamiembryo.cba.arizona.edu/.

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468 M. Pigliucci, M. Boudry

our intelligence by means of our language. To complicate matters further, there is

emerging empirical evidence that the human brain processes metaphors in a specific
fashion: research on Alzheimers patients, for instance (Amanzio et al. 2008), found that
impairment of the brains executive function, associated with the prefrontal cortex, leads
to poor understanding of novel metaphors (while, interestingly, comprehension of familiar
metaphors is unaffected). Metaphorical thinking seems to be a biologically entrenched
functional mode of our brains, and may therefore be hard to avoid altogether.
Both science and philosophy have made ample use of metaphorical and analogical
thinking, sometimes with spectacularly positive results, at other times more questionably
so. Nonetheless, it seems that nowhere is metaphorical thinking so entrenchedand so
potentially misleadingas in biology. Given the maturity of biology as a science, and
considering that it deals with objects whose nature is not as alien to our daily experience as,
say, those of quantum physics, we do not actually see any good reason for clinging onto
outdated metaphors in biological education and research for characterizing living organ-
isms, their genomes and their means of development. Taking into account the fact that the
machine/information metaphors have been grist to the mill of ID creationism, fostering
design intuitions and other misconceptions about living systems, we think it is time to
dispense with them altogether. Still, we are also not as naive as to expect that this advise
will be followed by scientists and science educators any time soon, precisely because the
machine/information metaphor is so entrenched in biology education. What to do then? We
propose two approaches, one for science educators, the other for practicing scientists.
In science education, talk of metaphorical thinking can be turned into a teaching
moment. Students (and the public at large) would actually greatly benefit from explana-
tions that contrast different metaphors with the express goal of highlighting the limitations
intrinsic in metaphors and analogies. So, for instance, science educators and writers could
talk about the human genome by introducing the blueprint metaphor, only to immediately
point out why it does not capture much of what genomes and organisms are about; they
could then proceed to familiarize their students and readers with alternative metaphors, say
the recipe one, focusing on differences with the original metaphor while of course not
neglecting to point out the (different) deficiencies of the new approach as well. The goal of
this process would be to foster a cautious attitude about metaphorical thinking, as well as to
develop a broader understanding of how unlike commonsense modern science really is. On
the latter point, it is interesting to note, for instance, that a popular refrain among evolution
or global warming deniers is that simple common sense shows that the scientists are
wrong, a position that ignores the proper weight of technical expertise in favor of a folk
understanding of nature. It is therefore crucial that the public appreciates the limitations of
common sense thinking about science.
There is an analogous teaching moment that can be brought to bear when research
scientists engage in unbridled metaphorical thinking: we could refer to this as a philoso-
phy-appreciation moment. Scientists are notoriously insensitive to, or even downright
dismissive of, considerations arising from the history and philosophy of their discipline,
and often for good practical reasons: modern science is a highly specialized activity, where
there is barely enough time to keep up with the overwhelming literature in ones own
narrow field of research, and certainly not enough incentive to indulge in historical
readings or philosophical speculation. Nonetheless, historians and philosophers of science
can easily show the pitfalls of metaphorical thinking (by using well-documented historical
examples) and even get across to their colleagues some basic notions of philosophy (by
analyzing the effects of particular metaphors on the development of specific lines of
scientific inquiry). None of this will quickly amount to overcoming C.P. Snows (1959)

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Why Machine-Information Metaphors are Bad for Science 469

infamous divide between the two cultures, but it may bring about better understanding
and appreciation of philosophy by scientists, and perhaps even help science see new
horizons that have been hitherto obscured by a superficially illuminating metaphor.

Acknowledgment The research of Maarten Boudry was supported by the Flemish Fund for Scientific
Research (FWO).

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